def handle_normal(mol_lst, args):
""" Writes replaced input files"""
inp = gaussian.Input()
for mol in mol_lst:
with open(mol, 'rb') as f:
old_input = f.read()
new_mol_name = atom_replace(mol, args)
inp.provide_existing_input_file(old_input)
inp.set_chk(fileutil.get_filename(new_mol_name))
inp.descript = atom_replace(inp.descript, args)
inp.geom = atom_replace(inp.geom, args)
inp.add_custom_basis_from_dic(CUSTOM_BASIS_LOCATION)
with open(new_mol_name, 'wb') as f:
inp.write(f)
def write_gau_min_file(folder_name, pymol, name, min_kwards, args):
"""Writes gaussian input min file"""
inp = gaussian.Input()
inp.provide_pymol(pymol)
inp.set_proc(args.proc)
inp.set_memory(args.memory)
inp.set_chk(name)
inp.set_kwards(min_kwards)
inp.set_description(name)
inp.set_charge(args.charge)
inp.set_mult(args.mult)
inp.add_custom_basis_from_dic(BASIS[args.basis])
with open(folder_name + '/' + name + '.com', 'wb') as f:
inp.write(f)
def handle_normal(args, mol, name, output_dir):
input_ = gaussian.Input()
if args.kwards:
kwards = args.kwards
else:
kwards = DEFAULT_KWRDS.format(args.solvent)
if args.ECP:
kwards += ' pseudo=read'
input_.set_kwards(kwards)
descrip = input_.descript + ' ' + args.descrip.format(args.solvent)
input_.set_description(descrip)
input_.set_chk(name)
shutil.copy2(mol[:-4] + '.' + args.chk,
output_dir + '/' + name + '.' + args.chk)
with open(output_dir + '/' + name + ".com", 'wb') as f:
input_.write(f)
def write_non_TS_mol(pymol, args, name):
inp = gaussian.Input()
inp.provide_pymol(pymol)
inp.set_proc(8)
inp.set_memory(4000)
inp.set_chk(name)
kwards = DEFAULT_KWRDS.format(args.solvent)
if args.ECP:
kwards += ' pseudo=read'
inp.set_kwards(kwards)
inp.set_description(name)
inp.set_charge(0)
inp.set_mult(args.mult)
inp.add_custom_basis_from_dic(args.basis)
with open(name + '.com', 'wb') as f:
inp.write(f)
def handle_TS(mol_name, args):
"""Accepts path to gaussian input TS molecule."""
with open(mol_name, 'rb') as f:
input = gaussian.Input()
input.provide_existing_input_file(f.read())
new_name = fileutil.add_to_name_but_keep_ext(mol_name, args.name)
input.set_chk(fileutil.get_filename(new_name))
if args.kwards:
kwrds = args.kwards
else:
kwrds = TS_KWRDS.format(args.solvent)
if args.ECP:
kwrds += ' pseudo=read'
input.set_kwards(kwrds)
input.add_custom_basis_from_dic(args.basis)
with open(os.path.realpath(args.dir) + '/' + new_name, 'wb') as f:
input.write(f)
def create_new_normal_input(mol, args, name):
"""Returns new input file."""
inp = gaussian.Input()
with open(mol, 'rb') as f:
inp.provide_existing_input_file(f.read())
inp.kwards = replace(args, inp.kwards)
if 'chkbas' not in inp.kwards:
inp.kwards += " chkbas"
if "geom=allcheck" not in inp.kwards:
inp.kwards += " geom=allcheck"
inp.kwards = stringutil.case_insensitive_replace(inp.kwards, ' gen ',
' genchk ')
inp.set_chk(fileutil.get_filename(name))
inp.set_geometry('')
inp.set_charge('')
inp.set_mult('')
inp.custom_basis = ''
print inp.kwards
return inp.write()
def main(argv):
args = process_command_line(argv)
gau_input = gaussian.Input()
gau_input.set_proc(args.proc)
gau_input.set_memory(args.memory)
if args.functional in FUNCTIONAL:
functional = FUNCTIONAL[args.functional]
else:
functional = args.functional
kwards = DEFAULT_KWRDS.format(functional) + SOLVENT_MODEL.format(
args.solvent)
gau_input.set_kwards(kwards)
for mol in args.input:
name = mol[:-4] + '_' + args.functional + '_' + args.basis
pymol = pybel.readfile(args.format, mol).next()
gau_input.provide_pymol(pymol)
gau_input.set_chk(name)
gau_input.add_custom_basis_from_dic(BASIS[args.basis])
with open(name + '.com', 'wb') as f:
gau_input.write(f)
def handle_mol(mol_name, args):
"""Accepts path to mol."""
if args.format != 'gau':
pymol = pybel.readfile(args.format, mol_name).next()
mol_txt = pymol.write('gau')
else:
with open(mol_name, 'rb') as f:
mol_txt = f.read()
mol_name_sans_ext = fileutil.get_filename(mol_name)
new_name = mol_name_sans_ext + args.suffix
std_input = gaussian.Input()
std_input.provide_existing_input_file(mol_txt)
std_input.set_chk(new_name)
std_input.set_proc(args.proc)
std_input.set_memory(args.memory)
std_input.set_charge(1)
kwards = create_kwards(pymol, args)
std_input.set_kwards(kwards)
#std_input.add_custom_basis_from_dic(BASIS[args.basis])
with open(new_name + '.com', 'wb') as f:
std_input.write(f)
def handle_mol(mol_name, args):
"""Accepts path to mol."""
if args.format != 'gau':
pymol = pybel.readfile(args.format, mol_name).next()
mol_txt = pymol.write('gau')
else:
with open(mol_name, 'rb') as f:
mol_txt = f.read()
mol_name_sans_ext = fileutil.get_filename(mol_name)
new_name = mol_name_sans_ext + args.name
std_input = gaussian.Input()
std_input.provide_existing_input_file(mol_txt)
std_input.set_chk(new_name)
if args.kwards:
kwrds = args.kwards
else:
kwrds = DEFAULT_KWRDS.format(args.solvent)
if args.ECP:
kwrds += ' pseudo=read'
std_input.set_kwards(kwrds)
std_input.add_custom_basis_from_dic(args.basis)
with open(os.path.realpath(args.dir) + '/' + new_name + '.com', 'wb') as f:
std_input.write(f)
def setup_converter(kwards, basis_path):
"""Creates converter object, which is used to prepare gaussian input
files"""
converter = gaussian.Input(kwards)
converter.set_custom_basis(basis_path)
return converter
